[petsc-dev] Inquiry about contributing to MMG interface

[neil liu]

Hi, Matt,

It is not enough to only turn on -the open boundary.
For the above example,  the 4 physical corner vertices (0D) for this
internal quadrilateral surface have to be set, otherwise the shape can not
be kept.
In addition, for my present case, the boundary edges (1D) consisting of
this quadrilateral surface need to be tagged.
The present bdLabel seems to only work for 2D shapes for 3D cases.
Please correct me if I am wrong.

Thanks,

Xiaodong

On Wed, Feb 5, 2025 at 12:05 PM Matthew Knepley <knepley at gmail.com> wrote:

> This is a really poor name. The boundary is not open in any sense. It
> should be called an internal boundary, and what they call internal
> boundaries should be called interdomain boundaries, but it seems too late
> to fix this.
>
> Turning on open boundaries is just a flag, so that is easy, and one can
> see the usefulness of this mode.
>
> My understanding from the documentation link below is that MMG does not
> change anything about parts of the mesh marked
> as internal boundaries, so we can read them right back out from the
> boundary label. Why would we need a new label for this?
>
>   Thanks,
>
>      Matt
>
> On Wed, Feb 5, 2025 at 11:22 AM Pierre Jolivet <pierre at joliv.et> wrote:
>
>> See also:
>> https://urldefense.us/v3/__https://www.mmgtools.org/mmg-remesher-try-mmg/mmg-remesher-tutorials/mmg-remesher-mmg3d/open-boundary-remeshing__;!!G_uCfscf7eWS!fwDKoY-5jpCBjuxT4xE9QxdGw3jTI-yozw_iUVJdxSJn7nQIb3OCvOiJI1EI4IGTufj_EY2QIoXIbyUCX-3uDw$ 
>> .
>>
>> Thanks,
>> Pierre
>>
>> On 5 Feb 2025, at 4:39 PM, neil liu <liufield at gmail.com> wrote:
>>
>> It seems the figures were  broken. Please see the following attached.
>>
>> On Wed, Feb 5, 2025 at 10:36 AM neil liu <liufield at gmail.com> wrote:
>>
>>> Hi, Mark,
>>>
>>> For example, in the left figure, the yellow rectangular face needs to be
>>> preserved during mesh refinement. However, without specifying its four
>>> corner points, the rectangle cannot be maintained, as shown in the right
>>> figure. Additionally, the four edges of this face must be recorded and
>>> retrieved for post-processing.
>>>
>>> This yellow face is an *open boundary*, meaning it is not an interface
>>> between different materials. To ensure its preservation during mesh
>>> refinement, MMG must be run in *opnbdy* (open boundary) mode.
>>>
>>> Thanks a lot,
>>>
>>> Xiaodong
>>> [image: image.png] [image: image.png]
>>>
>>>
>>> On Wed, Feb 5, 2025 at 10:05 AM Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>>
>>>> On Wed, Feb 5, 2025 at 9:52 AM neil liu <liufield at gmail.com> wrote:
>>>>
>>>>> Dear developers,
>>>>>
>>>>> I am currently working with MMG in the context of PETSc and have
>>>>> identified a need to modify the existing MMG interface,
>>>>> DMAdaptMetric_Mmg_Plex(), for our use case. Given these requirements,
>>>>> I would like to explore the feasibility of contributing to PETSc to enhance
>>>>> this interface, which has been verified and validated in our research code.
>>>>> *Proposed Modifications:*
>>>>>
>>>>>    1.
>>>>>
>>>>>    *Additional Labels for Physical Entities:*
>>>>>    - In addition to the existing bdLabel and rgLabel, our case
>>>>>       requires two additional labels to represent physical vertices and edges
>>>>>       within the computational domain (3D).
>>>>>
>>>>> I am open to this. Can you be more specific about what it means?
>>>>
>>>>>
>>>>>    1.
>>>>>       - One approach is to introduce two new parameters in the
>>>>>       subroutine’s input list. However, this may require modifications across
>>>>>       related components, such as Pragmatic.
>>>>>
>>>>> This is not a problem. I can modify those.
>>>>
>>>>>
>>>>>    1.
>>>>>
>>>>>    *Support for Open Boundaries:*
>>>>>    - The current interface does not support open boundaries, a
>>>>>       feature available in MMG.
>>>>>       - As a result, several MMG benchmark cases involving open
>>>>>       boundary remeshing cannot be executed within PETSc.
>>>>>
>>>>> Can you explain what this means? What is an open boundary exactly?
>>>>
>>>>
>>>>> Would this be a viable contribution to PETSc? If so, I would
>>>>> appreciate any guidance on the best approach to implementing these changes
>>>>> while maintaining compatibility with existing features.
>>>>>
>>>> Yes. Please make a fork of the petsc repo, make a branch with the
>>>> proposed changes, make an MR for that branch, and add me to your fork (I am
>>>> knepley on GitLab). I can help you get it going.
>>>>
>>>>   Thanks,
>>>>
>>>>     Matt
>>>>
>>>>
>>>>> Looking forward to your thoughts.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> Thanks,
>>>>> Xiaodong
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
>>>>
>>>> https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fwDKoY-5jpCBjuxT4xE9QxdGw3jTI-yozw_iUVJdxSJn7nQIb3OCvOiJI1EI4IGTufj_EY2QIoXIbyXoqpVOcQ$ 
>>>> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!anvbtQDqn57whvgg2qc1Dix0Izm9kxNlvUkeyYkcfknnt6VmqbCE0mlGSj6O1DLJx6qR7-7UsHv48zbaqVDECw$>
>>>>
>>> <The right figure.png><The left figure.png>
>>
>>
>>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fwDKoY-5jpCBjuxT4xE9QxdGw3jTI-yozw_iUVJdxSJn7nQIb3OCvOiJI1EI4IGTufj_EY2QIoXIbyXoqpVOcQ$ 
> <https://urldefense.us/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!fwDKoY-5jpCBjuxT4xE9QxdGw3jTI-yozw_iUVJdxSJn7nQIb3OCvOiJI1EI4IGTufj_EY2QIoXIbyVI8LSV4A$ >
>
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